DAMEfinder: DAMEfinder: Method to detect allele-specific methylation...
In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions
DAMEfinder R Documentation
DAMEfinder: Method to detect allele-specific methylation (ASM), and
differential ASM from Bisulfite sequencing data in R.
Description
The package allows the user to extract an ASM score in two ways: either from
a bismark bam file(s) and VCF file(s), or from the output from
methtuple. Either way the final output is a list of regions with
diferential allele-specific methylated between groups of samples of interest.
The package also provides functions to visualize ASM at the read level or the
score level
DAMEfinder functions
calc_asm extracts ASM for pairs of CpG
sites from a methtuple file, calc_derivedasm extracts ASM at each
CpG site linked to a SNP from the VCF file. Both functions generate a
RangedSummarizedExperiment, which is the input for the main function
find_dames, that generates a data.frame with regions
exhibiting differential ASM between a number of samples.
Author(s)
Stephany Orjuela sorjuelal@gmail.com
Dania Machlab
Mark D Robinson mark.robinson@imls.uzh.ch
markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.
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| DAMEfinder | R Documentation |
DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.
Description
The package allows the user to extract an ASM score in two ways: either from
a bismark bam file(s) and VCF file(s), or from the output from
methtuple. Either way the final output is a list of regions with
diferential allele-specific methylated between groups of samples of interest.
The package also provides functions to visualize ASM at the read level or the
score level
DAMEfinder functions
calc_asm extracts ASM for pairs of CpG
sites from a methtuple file, calc_derivedasm extracts ASM at each
CpG site linked to a SNP from the VCF file. Both functions generate a
RangedSummarizedExperiment, which is the input for the main function
find_dames, that generates a data.frame with regions
exhibiting differential ASM between a number of samples.
Author(s)
Stephany Orjuela sorjuelal@gmail.com
Dania Machlab
Mark D Robinson mark.robinson@imls.uzh.ch
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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